Dear Nora Kremer,
Your are missing the "!entry.URE.unit.connectivity" section in your .lib file, then atoms aren't connected or worst...
The following lines do the magic...
(AFTER !entry.URE.unit.connect)
!entry.URE.unit.connectivity table int atom1x int atom2x int flags
1 2 1
1 3 1
3 4 1
3 5 1
6 1 1
6 7 1
6 8 1
(BEFORE !entry.URE.unit.hierarchy)
If you want to visualize the actual connectivity of your AMBER system in VMD, then don't load the PDB file... as connectivity information is normally absent in such format, VMD will guess about it, which means it may connect things just because they a close enough... as you are building the system from well defined molecules (with reasonable bond distances), then you may be hidden any connectivity issues...
Instead, load the AMBER's topology and coordinates...
vmd ure.prmtop -rst7 ure.rst
Notice: topology must be named .prmtop for automatic detection, while I'm forcing VMD to read the ASCII AMBER format (rst7)
Last but not least, some molecules split through PBC in the "test.pdb" file, that may not be the best initial setup for AMBER...
Best,
MatÃas
PS: I don't know way people still uses the "old fashioned, heavy and restricted" ASCII format (.rst) instead of the "new fancy, light and flexible" NetCDF file format...
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Nora Kremer" <nora.kremer149.gmail.com>
Para: amber.ambermd.org
Enviados: Martes, 11 de Junio 2019 11:16:25
Asunto: [AMBER] Urea water mixture
Hello,
I'm actually trying to build a water-urea mixture box with different urea
concentrations.
I'm generating .prm and .rst files in tleap using the following input:
source leaprc.gaff
source leaprc.water.tip3p
loadamberparams frcmod.urea
loadamberparams frcmod.ionsjc_tip3p
loadoff urea_h.lib
URE = loadpdb test.pdb
set URE box { 22.336 22.336 23.445 }
savepdb URE test_2.pdb
saveamberparm URE ure.prm ure.rst
The urea_h.lib (-> urea_h) is attached. I did this myself by loading one
urea molecule into tleap and saving it as .lib file.
The test.pdb file is generated by a self written program.
Everything works fine, however, when saving the .prm and .rst files, I get
following warnings:
Warning: Unbonded Hydrogen atom H1 in URE.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
Warning: Unbonded Hydrogen atom H2 in URE.
Cannot determine the requested GB radius for this atom.
Writing the unmodified Bondi GB radius.
(I get this warning for all of the URE molecules)
So it seems like there are no bonds. When visualizing the output pdb file
in vmd, everything seems to be ok. However, when I try to start a
minimization run, it doesn't even start. I used the min.in input with other
systems, where it did work.
So, I don't see where I made mistakes (in tleap perhaps ?) and I hope, that
you can help me.
(I'm using the Amber18 package.)
Thank you
Nora
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Received on Tue Jun 11 2019 - 09:00:04 PDT
